The rules say "A successful defend will protect the Region and negate the Dire's ability"
In regard to the bolded, the sea serpent clearly has his ability kick in before the defense (as does the scorpion in the PnP). But all of the others (i.e. the ghost if someone is in the ruins to defend, the harpy if someone is in the mountains, etc.) would each be negated if a hero in that region defends for two health, right?
That is correct. The ability can be defended if not otherwise stated on the card.